#!/bin/bash
# Parameters.
db=/data2/projects/ht_study/ecoli_reference/blastdb/ecoli.fasta
segidx=/data2/projects/ht_study/ecoli_reference/segehmehl_idxs/ecoli.idx
ref=/data2/projects/ht_study/ecoli_reference/single/ecoli.fasta

query1=/data2/projects/ht_study/prepared_data/junct.fasta
query2=/data2/projects/ht_study/prepared_data/plain_1.fasta
query3=/data2/projects/ht_study/prepared_data/plain_2.fasta

#out1=/data2/projects/ht_study/blast_results/junct.txt
#out2=/data2/projects/ht_study/blast_results/plain_1.txt
#out3=/data2/projects/ht_study/blast_results/plain_2.txt
out1=/data2/projects/ht_study/segehmehl/junct.txt
out2=/data2/projects/ht_study/segehmehl/plain_1.txt
out3=/data2/projects/ht_study/segehmehl/plain_2.txt


# Executes blast on test data.
#blastall -a 10 -p blastn -d $db -i $query1 -m 8 -o $out1 -G 1 -E 1 &
#blastall -a 10 -p blastn -d $db -i $query2 -m 8 -o $out2 -G 1 -E 1 &
#blastall -a 10 -p blastn -d $db -i $query3 -m 8 -o $out3 -G 1 -E 1 &

segemehl.x -i $segidx -d $ref -q $query1 -H 2 -t 30 > $out1
segemehl.x -i $segidx -d $ref -q $query2 -H 2 -t 30 > $out2
segemehl.x -i $segidx -d $ref -q $query3 -H 2 -t 30 > $out3
